Reverting therapy resistance of lung cancer cells by forcing RNA:DNA hybrid formation

RNA:DNA hybrids are atypical RNA:DNA structures consisting of RNA:DNA hybrid and a displaced single-stranded DNA1. The formation of RNA:DNA hybrids is tightly linked to cancer formation and progression and has a significant contribution to the antineoplastic action of selected anti-cancer drugs. However, to date insights into the regulation of RNA:DNA hybrid management machineries in cancer cells and its relevance for therapy response and resistance are limited. Here, we use classic lung cancer model cells to study pathways that control RNA:DNA hybrid related genome instability triggered by the use of inhibitors of the DNA damage signalling kinase (ATR). Loss of ATR function is associated with an increase in RNA:DNA hybrid levels, drives DNA damage and reduces cancer cell viability. Importantly, adaptive resistance of lung cancer cells to ATR inhibitors is paralleled by improved RNA:DNA hybrid resolution, that significantly dampened the efficacy of pharmacological treatment. In order to identify drugs that break resistance to ATR inhibitor we performed a drug repositioning screening. We were able to identify a panel of drugs centring on TKIs (Gefitinib, Vandetanib and Imatinib) that re-sensitized ATR inhibitor resistant cells to the original treatment by triggering RNA:DNA hybrid driven DNA damage. Gene-expression analysis of drug responsive and resistant lung cancer cell lines revealed gene expression signatures that may explain the suppression of RNA:DNA hybrid formation in therapy-resistant cells. ATR inhibitors are actually in clinical trial for different solid tumor, among them for lung cancer. Our data will provide new insights into pathways that control RNA:DNA hybrid management in cancer cells but also individuate novel strategies to overcome cancer therapy resistance, the leading cause for cancer related patient death.